Rootkit TDSS.fa, all files marked as hidden and read-only, others

First off, thank you for this forum. I have followed the step-by-step directions as well as I was able (DDS would only run in safe mode), and I've provided the results below. Before finding this forum, I was trying to fix problems one at a time, which included removing the files and folders "hidden" and "read-only" attributes from the C: drive (via Properties, not attrib). I was also, rather randomly, running scans and whatnot, one of which identified MEM: Rootkit.Win32.TDSS.fa as well as others.

After completing Malwarebytes' scan and the other suggested scans, all scans are now indicating no infections found, but performance is still poor and several programs are showing erratic behavior such as not allowing a mouse click on active buttons within the program (Speed Up My PC and Stopzilla both display this behavior for instance). Please take a look and thanks in advance.

Uninstall Speed Up My PC.
Registry cleaners/optimizers are not recommended for several reasons:

Registry cleaners are extremely powerful applications that can damage the registry by using aggressive cleaning routines and cause your computer to become unbootable.

The Windows registry is a central repository (database) for storing configuration data, user settings and machine-dependent settings, and options for the operating system. It contains information and settings for all hardware, software, users, and preferences. Whenever a user makes changes to settings, file associations, system policies, or installed software, the changes are reflected and stored in this repository. The registry is a crucial component because it is where Windows "remembers" all this information, how it works together, how Windows boots the system and what files it uses when it does. The registry is also a vulnerable subsystem, in that relatively small changes done incorrectly can render the system inoperable. For a more detailed explanation, read Understanding The Registry.

Not all registry cleaners are created equal. There are a number of them available but they do not all work entirely the same way. Each vendor uses different criteria as to what constitutes a "bad entry". One cleaner may find entries on your system that will not cause problems when removed, another may not find the same entries, and still another may want to remove entries required for a program to work.

Not all registry cleaners create a backup of the registry before making changes. If the changes prevent the system from booting up, then there is no backup available to restore it in order to regain functionality. A backup of the registry is essential BEFORE making any changes to the registry.

Improperly removing registry entries can hamper malware disinfection and make the removal process more difficult if your computer becomes infected. For example, removing malware related registry entries before the infection is properly identified can contribute to system instability and even make the malware undetectable to removal tools.

The usefulness of cleaning the registry is highly overrated and can be dangerous. In most cases, using a cleaner to remove obsolete, invalid, and erroneous entries does not affect system performance but it can result in "unpredictable results".

Unless you have a particular problem that requires a registry edit to correct it, I would suggest you leave the registry alone. Using registry cleaning tools unnecessarily or incorrectly could lead to disastrous effects on your operating system such as preventing it from ever starting again.For routine use, the benefits to your computer are negligible while the potential risks are great.

I've uninstalled SpeedUpMyPC and Stopzilla. I thought MBAM was updated, but it wasn't so I ended up running it once, then updated it, then ran it again. Here are the results of the first MBAM scan and the second is below, followed by the DDS output.

Double click MBRCheck.exe to run (Vista and Windows 7 users, right click and select Run as Administrator).
It will show a black screen with some data on it.
Enter N to exit.
A report called MBRcheckxxxx.txt will be on your desktop
Open this report and post its content in your next reply.

**Note: In the event you already have Combofix, this is a new version that I need you to download. It is important that it is saved directly to your desktop**

Please, never rename Combofix unless instructed.

Close any open browsers.

Close/disable all anti virus and anti malware programs so they do not interfere with the running of ComboFix.

Very Important! Temporarily disable your anti-virus, script blocking and any anti-malware real-time protection before performing a scan. They can interfere with ComboFix or remove some of its embedded files which may cause "unpredictable results".

Click onthis linkto see a list of programs that should be disabled. The list is not all inclusive. If yours is not listed and you don't know how to disable it, please ask.

NOTE1. If Combofix asks you to install Recovery Console, please allow it.NOTE 2. If Combofix asks you to update the program, always do so.

Close any open browsers.

WARNING: Combofix will disconnect your machine from the Internet as soon as it starts

Please do not attempt to re-connect your machine back to the Internet until Combofix has completely finished.

If there is no internet connection after running Combofix, then restart your computer to restore back your connection.

Double click on combofix.exe & follow the prompts.

When finished, it will produce a report for you.

Please post the "C:\ComboFix.txt"

**Note 1: Do not mouseclick combofix's window while it's running. That may cause it to stall**Note 2 for AVG users: ComboFix will not run until AVG is uninstalled as a protective measure against the anti-virus. This is because AVG "falsely" detects ComboFix (or its embedded files) as a threat and may remove them resulting in the tool not working correctly which in turn can cause "unpredictable results". Since AVG cannot be effectively disabled before running ComboFix, the author recommends you to uninstall AVG first.
Use AppRemover to uninstall it: http://www.appremover.com/
We can reinstall it when we're done with CF.**Note 3: If you receive an error "Illegal operation attempted on a registery key that has been marked for deletion", restart computer to fix the issue.

Make sure, you re-enable your security programs, when you're done with Combofix.

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NOTE.
If, for some reason, Combofix refuses to run, try one of the following:

1. Run Combofix from Safe Mode.

2. Delete Combofix file, download fresh one, but rename combofix.exe to your_name.exeBEFORE saving it to your desktop.Do NOT run it yet.

Please download and run the below tool named Rkill(courtesy of BleepingComputer.com) which may help allow other programs to run.

There are 4 different versions. If one of them won't run then download and try to run the other one.

Vista and Win7 users need to right click Rkill and choose Run as Administrator

You only need to get one of these to run, not all of them. You may get warnings from your antivirus about this tool, ignore them or shutdown your antivirus.

NetSvcs: 6to4 - File not found
NetSvcs: AppMgmt - File not found
NetSvcs: HidServ - File not found
NetSvcs: Ias - File not found
NetSvcs: Iprip - File not found
NetSvcs: Irmon - File not found
NetSvcs: NWCWorkstation - File not found
NetSvcs: Nwsapagent - File not found
NetSvcs: WmdmPmSp - File not found

Note 1: UNCHECK any pre-checked toolbar and/or software offered with the Java update. The pre-checked toolbars/software are not part of the Java update.

Note 2: The Java Quick Starter (JQS.exe) adds a service to improve the initial startup time of Java applets and applications. If you don't want to run another extra service, go to Start > Control Panel > Java > Advanced > Miscellaneous and uncheck the box for Java Quick Starter. Click OK and restart your computer.

Uninstall SpeedUpMyPC.
Registry cleaners/optimizers are not recommended for several reasons:

Registry cleaners are extremely powerful applications that can damage the registry by using aggressive cleaning routines and cause your computer to become unbootable.

The Windows registry is a central repository (database) for storing configuration data, user settings and machine-dependent settings, and options for the operating system. It contains information and settings for all hardware, software, users, and preferences. Whenever a user makes changes to settings, file associations, system policies, or installed software, the changes are reflected and stored in this repository. The registry is a crucial component because it is where Windows "remembers" all this information, how it works together, how Windows boots the system and what files it uses when it does. The registry is also a vulnerable subsystem, in that relatively small changes done incorrectly can render the system inoperable. For a more detailed explanation, read Understanding The Registry.

Not all registry cleaners are created equal. There are a number of them available but they do not all work entirely the same way. Each vendor uses different criteria as to what constitutes a "bad entry". One cleaner may find entries on your system that will not cause problems when removed, another may not find the same entries, and still another may want to remove entries required for a program to work.

Not all registry cleaners create a backup of the registry before making changes. If the changes prevent the system from booting up, then there is no backup available to restore it in order to regain functionality. A backup of the registry is essential BEFORE making any changes to the registry.

Improperly removing registry entries can hamper malware disinfection and make the removal process more difficult if your computer becomes infected. For example, removing malware related registry entries before the infection is properly identified can contribute to system instability and even make the malware undetectable to removal tools.

The usefulness of cleaning the registry is highly overrated and can be dangerous. In most cases, using a cleaner to remove obsolete, invalid, and erroneous entries does not affect system performance but it can result in "unpredictable results".

Unless you have a particular problem that requires a registry edit to correct it, I would suggest you leave the registry alone. Using registry cleaning tools unnecessarily or incorrectly could lead to disastrous effects on your operating system such as preventing it from ever starting again.For routine use, the benefits to your computer are negligible while the potential risks are great.

That will take care of the first Eset finding.
The others are located on Combofix quarantine folder and in some of your restore points.
We'll take care of those with our next, last steps.

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Update Firefox to the latest 4.0 version.

Update Adobe Reader

You can download it from http://www.adobe.com/products/acrobat/readstep2.html
After installing the latest Adobe Reader, uninstall all previous versions.Note. If you already have Adobe Photoshop® Album Starter Edition installed or do not wish to have it installed UNcheck the box which says Also Download Adobe Photoshop® Album Starter Edition.

Alternatively, you can uninstall Adobe Reader (33.5 MB), download and install Foxit PDF Reader(3.5MB) from HERE.
It's a much smaller file to download and uses a lot less resources than Adobe Reader.Note: When installing FoxitReader, make sure to UN-check any pre-checked toolbar, or any other garbage.

6. Run Malwarebytes "Quick scan" once in a while to assure safety of your computer.

7. Run Temporary File Cleaner (TFC) weekly.

8. Download and install Secunia Personal Software Inspector (PSI): http://secunia.com/vulnerability_scanning/personal/. The Secunia PSI is a FREE security tool designed to detect vulnerable and out-dated programs and plug-ins which expose your PC to attacks. Run it weekly.

9. (optional) If you want to keep all your programs up to date, download and install FileHippo Update Checker.
The Update Checker will scan your computer for installed software, check the versions and then send this information to FileHippo.com to see if there are any newer releases.

Thanks so much for your support on this issue. While it seems the computer is no longer infected, it is displaying some rather severe abnormalities anyway. For instance, if I leave a program up for a few hours without touching it, like overnight, things start to go haywire. Programs won't execute, the Start button disappears, Turn Off Computer button disappears, Alt-f4 and reboot tells me I don't have permissions, etc. In general, it is useless until I get it restarted (sometimes a hard boot, sometimes just logging off/on works).

Anyway, I've reached the end of my patience and am going to reformat it and start over!